.. _`bio/bcftools/stats`:

BCFTOOLS STATS
==============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bcftools/stats?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/bcftools/stats

Generate VCF stats using bcftools stats.

**URL**: http://www.htslib.org/doc/bcftools.html#stats

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcf_stats:
        input:
            "{prefix}",
        output:
            "{prefix}.stats.txt",
        log:
            "{prefix}.bcftools.stats.log",
        params:
            "",
        wrapper:
            "v3.0.1/bio/bcftools/stats"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Notes
-----

* The `extra` param allows for additional program arguments (not `--threads`, `-f/--fasta-ref`, or `-o/--output`).
* For more information see, http://www.htslib.org/doc/bcftools.html#stats


Software dependencies
---------------------

* ``bcftools=1.18``
* ``snakemake-wrapper-utils=0.6.2``

Input/Output
------------
**Input:**

* BCF, VCF, or VCF.gz input

**Output:**

* stats text file




Authors
-------

* William Rowell
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "William Rowell"
    __copyright__ = "Copyright 2020, William Rowell"
    __email__ = "wrowell@pacb.com"
    __license__ = "MIT"


    from snakemake.shell import shell
    from snakemake_wrapper_utils.bcftools import get_bcftools_opts


    bcftools_opts = get_bcftools_opts(
        snakemake, parse_output=False, parse_output_format=False, parse_memory=False
    )
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    shell(
        "bcftools stats"
        " {bcftools_opts}"
        " {extra}"
        " {snakemake.input[0]}"
        " > {snakemake.output[0]}"
        " {log}"
    )


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